Thanks for your kind reply. To be clear of what I did, I used CYM as a
template to create a new residue in MCPB and generated charges for the
whole cluster, i.e Zn2+ along with the residues HHCC. In this process I
have restrained the charges of the backbone atoms to be equivalent to
parm99 and the charges on the side chain atoms were allowed to change
according to the presence of Zn2+.

Is this the correct way to proceed? Any suggestions in this regard would be
very helpful.